Novice Rstan user. Updated to R4.0 and re-installed Rstan according to web instructions.
Rcpp installed no problem
** testing if installed package keeps a record of temporary installation path
- DONE (Rcpp)
Did notice warnings with rstan
R> install.packages(“rstan”, type = “source”)
trying URL ‘https://cran.rstudio.com/src/contrib/rstan_2.19.3.tar.gz’
Content type ‘application/x-gzip’ length 922337 bytes (900 KB)
==================================================
downloaded 900 KB
- installing source package ‘rstan’ …
** package ‘rstan’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Core:535:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
Simple program no longer runs
R> model_string <- "
+ data {
+ // Number of data points
+ int n1;
+ int n2;
+ // Number of successes
+ int y1[n1];
+ int y2[n2];
+ }
+
+ parameters {
+ real<lower=0, upper=1> theta1;
+ real<lower=0, upper=1> theta2;
+ }
+
+ model {
+ theta1 ~ beta(1, 1);
+ theta2 ~ beta(1, 1);
+ y1 ~ bernoulli(theta1);
+ y2 ~ bernoulli(theta2);
+ }
+
+ generated quantities {
+ }
+ "
R> y1 <- c(0, 1, 0, 0, 0, 0, 1, 0, 0, 0)
R> y2 <- c(0, 0, 1, 1, 1, 0, 1, 1, 1, 0)
R> data_list <- list(y1 = y1, y2 = y2, n1 = length(y1), n2 = length(y2))
R>
R> library(rstan)
Loading required package: StanHeaders
Loading required package: ggplot2
Keep up to date with changes at https://www.tidyverse.org/blog/
rstan (Version 2.19.3, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
R> ###### This is maybe unnecessary
R> options(mc.cores = parallel::detectCores())
R> rstan_options(auto_write = TRUE)
R> # Compiling and producing posterior samples from the model.
R> stan_samples <- stan(model_code = model_string, data = data_list)
starting worker pid=54113 on localhost:11391 at 11:24:08.911
starting worker pid=54111 on localhost:11391 at 11:24:08.911
starting worker pid=54112 on localhost:11391 at 11:24:08.911
starting worker pid=54110 on localhost:11391 at 11:24:08.911
Error in unserialize(node$con) : error reading from connection
Calls: <Anonymous> -> slaveLoop -> makeSOCKmaster
Error in unserialize(node$con) : error reading from connection
Calls: <Anonymous> -> slaveLoop -> makeSOCKmaster
Error in unserialize(node$con) : error reading from connection
Calls: <Anonymous> -> slaveLoop -> makeSOCKmaster
Error in unserialize(node$con) : error reading from connection
Calls: <Anonymous> -> slaveLoop -> makeSOCKmaster
Execution halted
Execution halted
Execution halted
Execution halted
Error in makePSOCKcluster(names = spec, ...) :
Cluster setup failed. 4 of 4 workers failed to connect.
SessionInfo
R> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rstan_2.19.3 ggplot2_3.3.1 StanHeaders_2.21.0-3
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.12 pillar_1.4.4 compiler_4.0.0 prettyunits_1.1.1 tools_4.0.0 digest_0.6.25
[7] packrat_0.5.0 pkgbuild_1.0.8 lubridate_1.7.8 evaluate_0.14 lifecycle_0.2.0 tibble_3.0.1
[13] gtable_0.3.0 lattice_0.20-41 pkgconfig_2.0.3 rlang_0.4.6 Matrix_1.2-18 cli_2.0.2
[19] rstudioapi_0.11 parallel_4.0.0 yaml_2.2.1 xfun_0.14 loo_2.2.0 gridExtra_2.3
[25] withr_2.2.0 dplyr_0.8.5 knitr_1.28 generics_0.0.2 vctrs_0.3.1 stats4_4.0.0
[31] grid_4.0.0 tidyselect_1.1.0 glue_1.4.1 inline_0.3.15 R6_2.4.1 processx_3.4.2
[37] fansi_0.4.1 rmarkdown_2.1 callr_3.4.3 purrr_0.3.4 magrittr_1.5 codetools_0.2-16
[43] matrixStats_0.56.0 ps_1.3.3 scales_1.1.1 ellipsis_0.3.1 htmltools_0.4.0 assertthat_0.2.1
[49] colorspace_1.4-1 munsell_0.5.0 crayon_1.3.4
Thank you